IMAP-PART XX

A template for creating IMAP repositories

Fostering Reproducible Microbiome data Analysis with Snakemake workflow

General Overview

IMAP stands for Integrated Microbiome Analysis Pipelines, developed independenly as standalone GitHub repositories. When used sequentially, all IMAP parts provide a systematic microbiome data analysis beyond the traditional methods.

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Repo-specific RMD Chunks

Chunk 01

Chunk 02

Chunk 03

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Related work

Repo	Description	Status
IMAP-PART 01	preparing to getting started with microbiome data analysis	In-progress
IMAP-PART 02	How to download & explore microbiome sample metadata from NCBI-SRA Database	In-progress
IMAP-PART 03	How to download microbiome sequencing reads from NCBI-SRA Database	In-progress
IMAP-PART 04	Quality Control of Microbiome Next Generation Sequencing Reads	In-progress
IMAP-PART 05	Bioinformatics & classification of preprocessed microbiome sequencing data	In-progress
IMAP-PART 06	Microbial profiling using QIIME2 and Snakemake workflows	In-progress

Citation

Please consider citing the iMAP article^[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.

References

[1]

Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4

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Appendix

Project main tree

.
├── LICENSE
├── README.md
├── config
│   ├── config.yml
│   ├── pbs
│   ├── samples.tsv
│   ├── slurm
│   └── units.tsv
├── dags
├── data
├── images
│   ├── bkgd.png
│   ├── cicd.png
│   ├── imap.png
│   └── smkreport
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── imap.bib
│   └── references.bib
├── report
│   └── report.html
├── report.html
├── requirements.txt
├── resources
├── results
│   └── project_tree.txt
├── styles.css
├── templates
└── workflow
    ├── Snakefile
    ├── envs
    ├── rules
    ├── schemas
    └── scripts

18 directories, 18 files

Screenshot of interactive snakemake report

The interactive snakemake HTML report can be viewed by opening the report.html using any compatible browser. You will be able to explore the workflow and the associated statistics. You can close the left bar to get a more expansive display view.

Troubleshooting of FAQs

1. Question
Answer
2. Question
Answer

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Last updated on March 27, 2023.
Github_Repo: https://github.com/tmbuza/imap-smk-template.
Repo compiled and maintained by: Teresia Mrema-Buza.